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Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL ; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes.

Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles’ evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles’ evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.

Many venomous animals express toxins that show extraordinary levels of variation both within and among species. In snakes, most studies of venom variation focus on front-fanged species in the families Viperidae and Elapidae, even though rear-fanged snakes in other families vary along the same ecological axes important to venom evolution. Here we characterized venom gland transcriptomes from 19 snakes across two dipsadine rear-fanged genera (Leptodeira and Helicops, Colubridae) and two front-fanged genera (Bothrops, Viperidae; Micrurus, Elapidae). We compared patterns of composition, variation, and diversity in venom transcripts within and among all four genera. Venom gland transcriptomes of rear-fanged Helicops and Leptodeira and front-fanged Micrurus are each dominated by expression of single toxin families (C-type lectins, snake venom metalloproteinase, and phospholipase A2, respectively), unlike highly diverse front-fanged Bothrops venoms. In addition, expression patterns of congeners are much more similar to each other than they are to species from other genera. These results illustrate the repeatability of simple venom profiles in rear-fanged snakes and the potential for relatively constrained venom composition within genera.

• Admixture is a mechanism by which species of long-lived plants may acquire novel alleles. However, the potential role of admixture in the origin and maintenance of tropical plant diversity is unclear. We ask whether admixture occurs in an ecologically important clade of Eschweilera (Parvifolia clade, Lecythidaceae), which includes some of the most widespread and abundant tree species in Amazonian forests. • Using target capture sequencing, we conducted a detailed phylogenomic investigation of 33 species in the Parvifolia clade and investigated specific hypotheses of admixture within a robust phylogenetic framework. • We found strong evidence of admixture among three ecologically dominant species, E. coriacea, E. wachenheimii and E. parviflora, but a lack of evidence for admixture among other lineages. Accepted species were largely distinguishable from one another, as was geographic structure within species. • We show that hybridization may play a role in the evolution of the most widespread and ecologically variable Amazonian tree species. While admixture occurs among some species of Eschweilera, it has not led to widespread erosion of most species’ genetic or morphological identities. Therefore, current morphological based species circumscriptions appear to provide a useful characterization of the clade’s lineage diversity.

Premise Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications. Methods We used a hierarchical clustering approach, with tree‐based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene‐wise edge‐based analyses, concatenation, and coalescent‐based methods, and is summarized in a consensus framework. Results Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole‐genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications. Conclusions We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

Quercus alba L., also known as white oak, eastern white oak, or American white oak, is a quintessential North American species within the white oak section (Quercus) of the genus Quercus, subgenus Quercus. This species plays a vital role as a keystone species in eastern North American forests and plays a significant role in local and regional economies. As a long-lived woody perennial covering an extensive natural range, Q. alba’s biology is shaped by a myriad of adaptations accumulated throughout its natural history. Populations of Q. alba are crucial repositories of genetic, genomic, and evolutionary insights, capturing the essence of successful historical adaptations and ongoing responses to contemporary environmental challenges in the Anthropocene. This intersection offers an exceptional opportunity to integrate genomic knowledge with the discovery of climate-relevant traits, advancing tree improvement, forest ecology, and forest management strategies. This review provides a comprehensive examination of the current understanding of Q. alba’s biology, considering past, present, and future research perspectives. It encompasses aspects such as distribution, phylogeny, population structure, key adaptive traits to cyclical environmental conditions (including water use, reproduction, propagation, and growth), as well as the species’ resilience to biotic and abiotic stressors. Additionally, this review highlights the state-of-the-art research resources available for the Quercus genus, including Q. alba, showcasing developments in genetics, genomics, biotechnology, and phenomics tools. This overview lays the groundwork for exploring and elucidating the principles of longevity in plants, positioning Q. alba as an emerging model tree species, ideally suited for investigating the biology of climate-relevant traits.

The Neotropical clade of Lecythidaceae—Lecythidoideae—comprises 10 genera and more than 230 woody species that are usually rainforest trees. Lecythidoideae range from Mexico to southeast Brazil but are most diverse and abundant in the central Amazon and Guiana Shield regions. Previous studies found weak support for monophyly in the two species rich Amazon-centered genera, Eschweilera and Lecythis, and ambiguous relationships within the Bertholletia clade (Eschweilera, Lecythis, Bertholletia and Corythophora). We performed a phylogenomic analysis of Lecythidoideae with focus on the Bertholletia clade, using target capture sequencing of 343 nuclear loci and 10 informative plastome regions. Our sampling included 206 individuals from 130 described Neotropical species and ca. 10 undescribed taxa. Our limited sampling outside the Bertholletia clade confirmed the monophyly of Grias, Gustavia, Couroupita, Allantoma, Cariniana, and Couratari. Within the Bertholletia clade, however, our work shows that Lecythis and Eschweilera, as currently circumscribed, are polyphyletic. To align Lecythidaceae taxonomy with phylogeny, we propose six genus name changes within the former Lecythis and Eschweilera. Our new circumscription maintains the core Lecythis (Ollaria clade) and Eschweilera (Parvifolia clade). For the clade comprising the Poiteau and Chartacea sections of Lecythis we reinstate Chytroma Miers. For the former Pisonis section of Lecythis we reinstate Pachylecythis Ledoux. For the former Tetrapetala section of Eschweilera we propose Imbiriba gen. nov. For the Corrugata clade (formerly of Lecythis) we propose Guaiania gen. nov. We propose to elevate the Integrifolia clade of Eschweilera as a new genus, Scottmoria gen. nov. We determined that the Manaus-area endemic, Eschweilera amazoniciformis, is an isolated sister lineage to Corythophora and Imbiriba. We recognize this species as the monotypic genus Waimiria gen. nov. Our proposal for taxonomic changes highlights distinct evolutionary histories and eliminates paraphyletic and polyphyletic genera, resulting in 60 name changes for species or subspecies.

This dissertation represents a series of advances in plant systematics and molecular phylogenetics. Processes such as whole genome duplication, historical introgression, and rapid diversification shape the genomes of plants. I investigate these processes in the flowering plant lineage Ericales, a morphologically disparate group that includes kiwifruits, pitcher plants, obligate parasites, and ecologically dominate tropical tree lineages.Large genomic datasets offer the promise of resolving historically recalcitrant species relationships, but methods can yield conflicting results, especially when clades have experienced ancient, rapid diversification. In Chapter II, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications. Support for relationships among major clades was inferred from multiple lines of evidence and was summarized in a consensus framework. Our results supported a history largely concordant with previous studies but suggests that paleopolyploidy may be responsible for the remaining uncertainty. Our broad sampling allowed us to place the position of a whole genome duplication before the radiation of most ericalean families.Admixture is a mechanism by which populations of long-lived trees may acquire novel alleles. However, little is known about the genomes of most tropical tree species, or the extent to which they exchange genes. In Chapter III, we ask whether admixture occurs in an ecologically important clade of rainforest trees, the Parvifolia clade of Eschweilera (Lecythidaceae), which includes several of the most abundant tree species in Amazon forests. Using targeted sequence capture for hundreds of individuals from across Lecythidaceae, we conducted a detailed phylogenomic investigation of the Parvifolia clade. We implement a novel workflow to test for admixture in target capture datasets. We found strong evidence of admixture among three ecologically dominant species but a lack of evidence for widespread genomic admixture in most lineages. Species were distinguishable from one another based on our sequencing targets, as was geographic structure within species.Biogeography informs our understanding of patterns of global species diversity and the processes that shape them, but such inferences strongly rely on the quality of the genomic and fossil information employed. In Chapter IV, we use targeted sequence capture to collect data from species across Ericales, as well as the available fossil information, to investigate the origin and diversification of the primrose family (Primulaceae). We present updated phylogenetic and biogeographic hypotheses for the family and show that genomic evidence contradicts previous biogeographic inference based on morphology. Our results show that a major taxonomic revision of Ardisia and at least 19 closely related genera is required to circumscribe monophyletic genera.While this dissertation advances our understanding of the evolution of Ericales, it has also revealed unanswered questions about the phylogeny of the order and the processes that have generated the groups diversity. Paleopolyploidy, rapid radiation, admixture, and long-distance dispersal are among the factors that have contributed to the evolution of the clade. Future work is needed to better characterize the relative importance of these factors and to continue refining the taxonomy of various clades within Ericales.

Premise of the study: Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Methods: Using a broad sampling of angiosperm plastomes, we characterized gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). Key results: We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find gene length is the strongest correlate to concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Conclusions: Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given the documented cases of heteroplasmic recombination. We suggest rpoC2 as a useful marker for reconstructing angiosperm phylogeny, reducing the effort and expense of assembling and analyzing entire plastomes.

While DNA has built the framework for molecular insights from museum collections, the utility of archival RNA remains largely unexplored. Likely a consequence of the known instability of RNA relative to DNA, this has effectively nullified the use of herbaria for transcriptomics. Here, we challenge the assumption that herbaria cannot be used for transcriptomics by assembling transcriptomes from RNA extracted from herbarium specimens. Through systematic comparison of transcriptomes from fresh-collected, silica-dried, and archival specimens, we demonstrate the suitability of herbarium-derived RNA for transcriptomics. The practical applicability of archival mRNA was further illustrated by the functional validation of a plant immune receptor synthesized from a specimen collected in 1956. These results contradict the community consensus regarding archival RNA and open the door to subsequent transcriptomic explorations in rare and extinct species. Our findings highlight the importance of preserving and utilizing the diversity embedded within herbarium collections.Competing Interest StatementThe authors have declared no competing interest.Footnotes* Additional quality analyses have been performed* https://zenodo.org/records/14720388